add rotl logo

.Rbuildignore

@@ -17,3 +17,4 @@ revdep/
 ^tic.R$
 ^.pre-commit-config.yaml$
 ^\.github$
+^CRAN-SUBMISSION$

README.Rmd

@@ -19,7 +19,7 @@ opts_knit$set(upload.fun = imgur_upload)
 <!-- badges: end -->
 
 
-# An R interface to Open Tree API
+# rotl: An R interface to Open Tree API <img src="man/figures/logo.svg" align="right" />
 
 `rotl` is an R package to interact with the Open Tree of Life data APIs. It was
 initially developed as part of the

README.md

@@ -14,7 +14,7 @@ developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.re
 
 <!-- badges: end -->
 
-# An R interface to Open Tree API
+# rotl: An R interface to Open Tree API <img src="man/figures/logo.svg" align="right" />
 
 `rotl` is an R package to interact with the Open Tree of Life data APIs.
 It was initially developed as part of the [NESCENT/OpenTree/Arbor
@@ -50,14 +50,14 @@ remotes::install_github("ropensci/rotl")
 
 There are three vignettes:
 
-  - Start by checking out the “How to use `rotl`?” by typing:
+-   Start by checking out the “How to use `rotl`?” by typing:
     `vignette("rotl", package="rotl")` after installing the package.
 
-  - Then explore how you can use `rotl` with other packages to combine
+-   Then explore how you can use `rotl` with other packages to combine
     your data with trees from the Open Tree of Life project by typing:
     `vignette("data_mashups", package="rotl")`.
 
-  - The vignette “Using the Open Tree Synthesis in a comparative
+-   The vignette “Using the Open Tree Synthesis in a comparative
     analsysis” demonstrates how you can reproduce an analysis of a
     published paper by downloading the tree they used, and data from the
     supplementary material: `vignette("meta-analysis", package="rotl")`.
@@ -92,7 +92,7 @@ apes <- c("Pongo", "Pan", "Gorilla", "Hoolock", "Homo")
     ## 5          homo        Homo             FALSE 770309      FALSE sibling_higher
     ##   number_matches
     ## 1              2
-    ## 2              1
+    ## 2              2
     ## 3              1
     ## 4              1
     ## 5              1
@@ -113,22 +113,12 @@ tr <- tol_induced_subtree(ott_ids = ott_id(resolved_names))
 plot(tr)
 ```
 
-![](https://i.imgur.com/5Fdb927.png)<!-- -->
+![](https://i.imgur.com/xTsGAz8.png)<!-- -->
 
 The code above can be summarized in a single pipe:
 
 ``` r
 library(magrittr)
-```
-
-    ## 
-    ## Attaching package: 'magrittr'
-
-    ## The following objects are masked from 'package:testthat':
-    ## 
-    ##     equals, is_less_than, not
-
-``` r
 ## or expressed as a pipe:
 c("Pongo", "Pan", "Gorilla", "Hoolock", "Homo") %>%
   tnrs_match_names() %>%
@@ -143,7 +133,7 @@ c("Pongo", "Pan", "Gorilla", "Hoolock", "Homo") %>%
     ## mrcaott83926ott3607689, mrcaott83926ott3607732, mrcaott770295ott3607719,
     ## mrcaott770295ott3607692, Ponginae ott1082538, Hylobatidae ott166544
 
-![](https://i.imgur.com/43LgNKf.png)<!-- -->
+![](https://i.imgur.com/rQmAgaa.png)<!-- -->
 
 ## Citation and Manuscript
 
@@ -191,4 +181,4 @@ Please note that this project is released with a [Contributor Code of
 Conduct](https://github.com/ropensci/rotl/blob/master/CONDUCT.md). By
 participating in this project you agree to abide by its terms.
 
-[![](https://ropensci.org/public_images/github_footer.png)](https://ropensci.org)
+[![](https://ropensci.org/public_images/github_footer.png)](https://ropensci.org/)